Water battles in the Sacramento-San Joaquin Delta have been fought over a basic question: as the state’s thirsty cities and farms demand more Delta water, is there enough left for endangered fish like the Delta smelt and chinook salmon?

In a report released today from the Bay Institute, environmentalists argue that the damage being done to the Delta ecosystem from removing water isn't fully being measured.

Two-thirds of Californians get their water from the Delta, the inland complex of islands and channels where the Sacramento and San Joaquin rivers come together, carrying runoff from tributaries and the Sierra Nevada snowpack. Two huge plants in the southern Delta can pump out tens of thousand of gallons of water per second, sending most of it to San Joaquin Valley farms and Southern California cities.

The water heading to the pumps contains fish. To prevent the fish from being ground up by the pumps, the water flows through special screening facilities, the Skinner Fish Facility and the Tracy Fish Facility. As many as 15 million fish per year are “salvaged” or captured at these screens. The fish are then loaded into trucks and released elsewhere in the Delta.

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The problem, says Jon Rosenfield, a biologist with the Bay Institute, is that freshwater also contains smaller organisms. “The salvage facilities don’t count fish eggs or really small larval fish,” he says. “You can’t remove between 50 and 70 percent of the water in a system and not take out a very large fraction of the food that’s in that water.”

The report authors argue that removing organisms at the bottom of the food chain has a huge impact. “We have an ecosystem that’s in a free fall and we’re making the situation worse by exporting the fish food,” says Rosenfield.

Rosenfield also points to the fish that get eaten before they get to the salvage facility. “Before they get to the screens, there are whole bunch of predators,” he says. “The actual numbers of fish and fish food that are getting removed from the system are from 4 to 10 times higher than the number of fish that get counted.”

Whether or not Delta smelt and other fish survive the salvage process is another big question. “Very few fish are able to tolerate that much handling and transport in a truck,” says Rosenfield. Researchers have attempted to measure how many fish are killed in the process and operators at the pumping facilities are currently looking at ways improve the survival rate of the fish that are caught. Thanks to extremely wet weather last year, the Delta smelt population rebounded slightly after a decade of decline.

Some water agencies claim that pumping freshwater isn’t to blame for the decline of endangered species. "We've focused on the pumps excessively. We’ve ignored the issues of toxics and predators and other things," says Jason Peltier of the Westlands Water District, a largely agricultural district that relies on Delta water.

“The main driving factor for fish decline is lack of food in the system, driven by Asian clams in the western Delta that are filter feeders. That’s taking a lot of the food chain. In addition, maybe the discharge of ammonia from wastewater treatment plants has disrupted the lower end of the food chain,” he says.

The science of endangered species recovery is back in the spotlight this year, as the state writes two plans for the future of the Delta, the Delta Plan and the Bay Delta Conservation Plan. “This is the most critical period in two decades. California is coming to grips with the fact that its water supply system is unsustainable,” says Rosenfield.

Rosenfield says he’s not against it in principal, but says it will only work “if it’s designed right and if it’s limited in the amount of water that it diverts from the Delta. It’s not really going to solve the problem unless enough water is left in the Delta.”